Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014369.1 Kokia drynarioides strain JFW-HI SEQ_129406, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 29057
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:64 original size:39 final size:39
Alignment explanation
Indices: 21--143 Score: 131
Period size: 39 Copynumber: 3.2 Consensus size: 39
11 TGCAACCATT
* *
21 CAATCTCTTACCTCAAGGCTGAGGCAGATCACCATCAGC
1 CAATCTCTTACCTCGAGCCTGAGGCAGATCACCATCAGC
* * ** **
60 CAATCTCTTACCCCGAGCCTGGGGCAGAT-TGCAGTCATT
1 CAATCTCTTACCTCGAGCCTGAGGCAGATCACCA-TCAGC
* * *
99 CGATCTCTTACCTCGAGCCTGAGGCAGATCATCATTAGC
1 CAATCTCTTACCTCGAGCCTGAGGCAGATCACCATCAGC
138 CAATCT
1 CAATCT
144 TTCACCTGAT
Statistics
Matches: 65, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
38 2 0.03
39 61 0.94
40 2 0.03
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
CAATCTCTTACCTCGAGCCTGAGGCAGATCACCATCAGC
Found at i:644 original size:18 final size:17
Alignment explanation
Indices: 621--663 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
611 TTAAATTGGT
*
621 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-GTTTAAA
639 TTTAAATTTAGTTTAAA
1 TTTAAATTTAGTTTAAA
656 TTTGAAAT
1 TTT-AAAT
664 GATTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAGTTTAAA
Found at i:670 original size:17 final size:17
Alignment explanation
Indices: 593--677 Score: 56
Period size: 17 Copynumber: 5.3 Consensus size: 17
583 AACTTTTGAT
* * *
593 TTTAAATTTATATTAAG
1 TTTAAATTGATTTTAAA
*
610 TTTAAATTGGTTTTAAA
1 TTTAAATTGATTTTAAA
627 TTT--A-T--TTTTAAA
1 TTTAAATTGATTTTAAA
* *
639 TTTAAATTTAGTTTAAA
1 TTTAAATTGATTTTAAA
656 TTTGAAA-TGATTTTAAA
1 TTT-AAATTGATTTTAAA
*
673 CTTAA
1 TTTAA
678 TTTAAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
12 10 0.19
14 2 0.04
15 2 0.04
16 2 0.04
17 35 0.65
18 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (17 bp):
TTTAAATTGATTTTAAA
Found at i:670 original size:46 final size:46
Alignment explanation
Indices: 593--694 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
583 AACTTTTGAT
* * * * *
593 TTTAAATTTATATTAAGTTTAAATTGGTTTTAAATTTATTTTTAAA
1 TTTAAATTTATATTAAATTTAAATTGATTTTAAACTTAATTTAAAA
639 TTTAAATTTAGT-TTAAATTTGAAA-TGATTTTAAACTTAATTTAAAA
1 TTTAAATTTA-TATTAAATTT-AAATTGATTTTAAACTTAATTTAAAA
*
685 TTTTAATTTA
1 TTTAAATTTA
695 AAAAGTCCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
46 44 0.92
47 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (46 bp):
TTTAAATTTATATTAAATTTAAATTGATTTTAAACTTAATTTAAAA
Found at i:1313 original size:3 final size:3
Alignment explanation
Indices: 1305--1333 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1295 AAATATTTTA
1305 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1334 AAGAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2251 original size:29 final size:30
Alignment explanation
Indices: 2196--2275 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
2186 TGTCCAAAGA
**
2196 TCCCTAAA-TTTCCAAAAATCATGATTTAAC
1 TCCC-AAACTTTCCAAAAATCAAAATTTAAC
* *
2226 -CCCAAACTTTCCAAAAATTAAAATTTGAC
1 TCCCAAACTTTCCAAAAATCAAAATTTAAC
* *
2255 TCCCAATCTTTTCAAAAATCA
1 TCCCAAACTTTCCAAAAATCA
2276 CATTTTGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.07
29 21 0.51
30 17 0.41
ACGTcount: A:0.41, C:0.25, G:0.03, T:0.31
Consensus pattern (30 bp):
TCCCAAACTTTCCAAAAATCAAAATTTAAC
Found at i:2283 original size:30 final size:30
Alignment explanation
Indices: 2196--2284 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
2186 TGTCCAAAGA
** *
2196 TCCCTAAA-TTTCCAAAAATCATGATTTAAC
1 TCCC-AAACTTTCCAAAAATCAAAATTTGAC
*
2226 -CCCAAACTTTCCAAAAATTAAAATTTGAC
1 TCCCAAACTTTCCAAAAATCAAAATTTGAC
* * * *
2255 TCCCAATCTTTTCAAAAATCACATTTTGAC
1 TCCCAAACTTTCCAAAAATCAAAATTTGAC
2285 CCTCGAACTA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
28 3 0.06
29 21 0.44
30 24 0.50
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (30 bp):
TCCCAAACTTTCCAAAAATCAAAATTTGAC
Found at i:2316 original size:29 final size:28
Alignment explanation
Indices: 2267--2885 Score: 289
Period size: 29 Copynumber: 21.2 Consensus size: 28
2257 CCAATCTTTT
* *
2267 CAAAAATCACATTTTGACCCTCGAACTAC
1 CAAAAATTACATTTT-ACCCTCGAACTTC
2296 ACAAAAATTACATTTTACCCTCGAACTTC
1 -CAAAAATTACATTTTACCCTCGAACTTC
* * * *
2325 ACAAAAATTATATTTTTGCCCCCCAACTTTC
1 -CAAAAATTACA-TTTTACCCTCGAAC-TTC
*
2356 CAAAAATTACATTTTACCCTTGAACTTC
1 CAAAAATTACATTTTACCCTCGAACTTC
** * *
2384 CAAAAAATCGCATTTTTGCCCTCAAACTTC
1 C-AAAAATTACA-TTTTACCCTCGAACTTC
* *
2414 CAAAAATTTTCA-TTTACCCCCGAACTTC
1 CAAAAA-TTACATTTTACCCTCGAACTTC
*
2442 CAAAAA-TATCATTCTTGACCC-CGAACTTTT
1 CAAAAATTA-CATT-TT-ACCCTCGAAC-TTC
* * * * *
2472 CAAAAATTACCGTTTTGCTCTTGAA-TTT
1 CAAAAATTA-CATTTTACCCTCGAACTTC
* * *
2500 CAAAAATTTACCATTTTATCTTCGAATTTC
1 CAAAAA-TTA-CATTTTACCCTCGAACTTC
*
2530 CAAAAATTTCATTTTTGA-CCTCGAACTTTC
1 CAAAAATTACA-TTTT-ACCCTCGAAC-TTC
* * * *
2560 AAAAAATTACCTTTTTACCCTTAGAA-GTC
1 CAAAAATTA-CATTTTACCC-TCGAACTTC
* *
2589 CAAAAATTCCATTTTAACCCT-AAACTTTC
1 CAAAAATTACATTTT-ACCCTCGAAC-TTC
* * * *
2618 AAAAAATAACATTTTACCCTTGAACTAC
1 CAAAAATTACATTTTACCCTCGAACTTC
* * * *
2646 CAAAAAATCAAATTTTTACCC-CTAAACTTT
1 C-AAAAATTACA-TTTTACCCTC-GAACTTC
*
2676 AAAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTA-CATTTTACCCTCGAACTTC
*
2705 CAAAAA-TATCATTTTTAACCC-C-AAATTC
1 CAAAAATTA-CA-TTTT-ACCCTCGAACTTC
2733 TCTAAAAATTACCATTTTACCC-C-AAGCTTC
1 -C-AAAAATTA-CATTTTACCCTCGAA-CTTC
* * * * * *
2763 TAGAAATTGCTTTTCTTACCCCCG-AGTGTC
1 CAAAAATTAC-ATT-TTACCCTCGAACT-TC
* * *
2793 CAAAAAATACCATTTTACCCTTGAAATGTC
1 CAAAAATTA-CATTTTACCCTCGAACT-TC
* * *
2823 C-AAAATTACCGTTTTACCTTCGAACCTC
1 CAAAAATTA-CATTTTACCCTCGAACTTC
* *
2851 CAAAAATTACCATTTTACCCCCG-ACATC
1 CAAAAATTA-CATTTTACCCTCGAACTTC
2879 CAAAAAT
1 CAAAAAT
2886 CGTATTTTTG
Statistics
Matches: 453, Mismatches: 93, Indels: 88
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.00
27 5 0.01
28 79 0.17
29 208 0.46
30 142 0.31
31 18 0.04
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (28 bp):
CAAAAATTACATTTTACCCTCGAACTTC
Found at i:2330 original size:59 final size:57
Alignment explanation
Indices: 2268--2719 Score: 282
Period size: 59 Copynumber: 7.8 Consensus size: 57
2258 CAATCTTTTC
* *
2268 AAAAATCACATTTTGACCCTCGAACTACACAAAAATTACATTTTACCCTCGAACTTCA
1 AAAAATTACATTTTGACCCTCGAACTTC-CAAAAATTACATTTTACCCTCGAACTTCA
* * * *
2326 CAAAAATTATATTTTTG-CCCCCCAACTTTCCAAAAATTACATTTTACCCTTGAACTTCCA
1 -AAAAATTACA-TTTTGACCCTCGAAC-TTCCAAAAATTACATTTTACCCTCGAACTT-CA
** * * * *
2386 AAAAATCGCATTTTTG-CCCTCAAACTTCCAAAAATTTTCA-TTTACCCCCGAACTTCC
1 AAAAATTACA-TTTTGACCCTCGAACTTCCAAAAA-TTACATTTTACCCTCGAACTTCA
* * * * * *
2443 AAAAA-TATCATTCTTGACCC-CGAACTTTTCAAAAATTACCGTTTTGCTCTTGAATTTCA
1 AAAAATTA-CATT-TTGACCCTCGAAC-TTCCAAAAATTA-CATTTTACCCTCGAACTTCA
* * * * *
2502 AAAATTTACCATTTT-ATCTTCGAATTTCCAAAAATTTCATTTTTGA-CCTCGAACTTTCA
1 AAAAATTA-CATTTTGACCCTCGAACTTCCAAAAATTACA-TTTT-ACCCTCGAAC-TTCA
* * * * * *
2561 AAAAATTACCTTTTTACCCTTAGAA-GTCCAAAAATTCCATTTTAACCCT-AAACTTTCA
1 AAAAATTACATTTTGACCC-TCGAACTTCCAAAAATTACATTTT-ACCCTCGAAC-TTCA
* * * * * * *
2619 AAAAATAACATTTT-ACCCTTGAACTACCAAAAAATCAAATTTTTACCC-CTAAACTTTA
1 AAAAATTACATTTTGACCCTCGAACTTCC-AAAAATTACA-TTTTACCCTC-GAACTTCA
2677 AAAAATTACCATTTT-ACCCTCGAACTTCCAAAAA-TATCATTTT
1 AAAAATTA-CATTTTGACCCTCGAACTTCCAAAAATTA-CATTTT
2720 TAACCCCAAA
Statistics
Matches: 306, Mismatches: 62, Indels: 52
0.73 0.15 0.12
Matches are distributed among these distances:
56 6 0.02
57 29 0.09
58 112 0.37
59 140 0.46
60 19 0.06
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (57 bp):
AAAAATTACATTTTGACCCTCGAACTTCCAAAAATTACATTTTACCCTCGAACTTCA
Found at i:2726 original size:59 final size:59
Alignment explanation
Indices: 2497--2754 Score: 262
Period size: 59 Copynumber: 4.4 Consensus size: 59
2487 TGCTCTTGAA
* * * * * * * *
2497 TTTCAAAAATTTACCATTTTATCTTCGAATTTCCAAAAATTTCATTTTTGACCTCGAAC
1 TTTCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATATCATTTTTAACCCCAAAC
* * * *
2556 TTTCAAAAAATTACCTTTTTACCCTTAGAA-GTCCAAAAAT-TCCA-TTTTAACCCTAAAC
1 TTTCAAAAAATTACCATTTTACCC-TCGAACTTCCAAAAATAT-CATTTTTAACCCCAAAC
* * *
2614 TTTCAAAAAA-TAACATTTTACCCTTGAACTACCAAAAA-ATCAAATTTTT-ACCCCTAAAC
1 TTTCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATATC--ATTTTTAACCCC-AAAC
2673 TTT-AAAAAATTACCATTTTACCCTCGAACTTCCAAAAATATCATTTTTAACCCCAAA-
1 TTTCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATATCATTTTTAACCCCAAAC
*
2730 TTCTCTAAAAATTACCATTTTACCC
1 TT-TCAAAAAATTACCATTTTACCC
2755 CAAGCTTCTA
Statistics
Matches: 166, Mismatches: 20, Indels: 26
0.78 0.09 0.12
Matches are distributed among these distances:
56 5 0.03
57 21 0.13
58 42 0.25
59 91 0.55
60 7 0.04
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
TTTCAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATATCATTTTTAACCCCAAAC
Found at i:2755 original size:88 final size:87
Alignment explanation
Indices: 2426--2755 Score: 253
Period size: 88 Copynumber: 3.8 Consensus size: 87
2416 AAAATTTTCA
* * * * *
2426 TTTACCCCCGAACTTCCAAAAATATCATTCTTGACCCCGAACTTTTC-AAAAATTACCGTTTTGC
1 TTTACCCTCGAACTTCCAAAAATATCATTTTTGACCCC-AACTTCTCAAAAAATTACCATTTTAC
* * * *
2490 TCTTGAATTTCAAAAATTTACCAT
65 CCCTAAATTT-AAAAAATTACCAT
* * * * * *
2514 TTTATCTTCGAATTTCCAAAAATTTCATTTTTGACCTCGAACTT-TCAAAAAATTACCTTTTTAC
1 TTTACCCTCGAACTTCCAAAAATATCATTTTTGACC-CCAACTTCTCAAAAAATTACCATTTTAC
* * **
2578 CCTTAGAAGTCCAAAAATT-CCAT
65 CCCTA-AATTTAAAAAATTACCAT
* * * * * * *
2601 TTTAACCCT-AAACTTTCAAAAAATAACA-TTTT-ACCCTTGAACTAC-CAAAAAATCA-AATTT
1 TTT-ACCCTCGAAC-TTCCAAAAATATCATTTTTGACCC--CAACTTCTCAAAAAATTACCA-TT
2661 TTACCCCTAAACTTTAAAAAATTACCAT
61 TTACCCCTAAA-TTTAAAAAATTACCAT
* * *
2689 TTTACCCTCGAACTTCCAAAAATATCATTTTTAACCCCAAATTCTCTAAAAATTACCATTTTACC
1 TTTACCCTCGAACTTCCAAAAATATCATTTTTGACCCCAACTTCTCAAAAAATTACCATTTTACC
2754 CC
66 CC
2756 AAGCTTCTAG
Statistics
Matches: 187, Mismatches: 39, Indels: 32
0.72 0.15 0.12
Matches are distributed among these distances:
85 1 0.01
86 5 0.03
87 68 0.36
88 104 0.56
89 9 0.05
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (87 bp):
TTTACCCTCGAACTTCCAAAAATATCATTTTTGACCCCAACTTCTCAAAAAATTACCATTTTACC
CCTAAATTTAAAAAATTACCAT
Found at i:4974 original size:17 final size:17
Alignment explanation
Indices: 4952--4985 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4942 CTAAGAATTT
4952 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
4969 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
4986 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:5672 original size:23 final size:23
Alignment explanation
Indices: 5644--5701 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
5634 CGTCCGTCCT
5644 TGCTGACTAGATATTCTAGAAGC
1 TGCTGACTAGATATTCTAGAAGC
* **
5667 TGCTGACTGGACCTTCTAGAAGC
1 TGCTGACTAGATATTCTAGAAGC
*
5690 TGTTGACTAGAT
1 TGCTGACTAGAT
5702 GCCACGTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (23 bp):
TGCTGACTAGATATTCTAGAAGC
Found at i:6412 original size:19 final size:21
Alignment explanation
Indices: 6380--6425 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
6370 TAAGCAACCA
6380 TTTTTTCATCTTTTTCTCCTT
1 TTTTTTCATCTTTTTCTCCTT
*
6401 TTTTTTC-T-TTTTTTTCCTT
1 TTTTTTCATCTTTTTCTCCTT
*
6420 TCTTTT
1 TTTTTT
6426 AGAACCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 1 0.04
21 7 0.30
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTCATCTTTTTCTCCTT
Found at i:22364 original size:44 final size:44
Alignment explanation
Indices: 22305--22393 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
22295 CTGAGATGTT
22305 TCCATTTATTAGCATGAACTAAATTCCTAAATACCTAGGGGAGA
1 TCCATTTATTAGCATGAACTAAATTCCTAAATACCTAGGGGAGA
22349 TCCATTTATTAGCATGAACTAAATTCCTAAATACCTAGGGGAGA
1 TCCATTTATTAGCATGAACTAAATTCCTAAATACCTAGGGGAGA
22393 T
1 T
22394 GAACCCTAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (44 bp):
TCCATTTATTAGCATGAACTAAATTCCTAAATACCTAGGGGAGA
Found at i:25849 original size:5 final size:5
Alignment explanation
Indices: 25839--25881 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
25829 TTTATTATCA
* *
25839 ATTTT ATTTT ATTTT ATCTT ATATT ATTTT CAATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT --ATTTT ATTTT A
25882 GTTATGCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 28 0.85
7 5 0.15
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (5 bp):
ATTTT
Found at i:25851 original size:17 final size:17
Alignment explanation
Indices: 25829--25886 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
25819 AATTAGTATA
25829 TTTATTATCAATTTTAT
1 TTTATTATCAATTTTAT
* *
25846 TTTATT-T-TATCTTAT
1 TTTATTATCAATTTTAT
* *
25861 ATTATTTTCAATTTTAT
1 TTTATTATCAATTTTAT
25878 TTTAGTTAT
1 TTTA-TTAT
25887 GCACTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
15 11 0.35
16 2 0.06
17 15 0.48
18 3 0.10
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTATCAATTTTAT
Found at i:27737 original size:23 final size:25
Alignment explanation
Indices: 27711--27756 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27701 GCAATTAGGG
27711 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
27734 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
27757 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Done.